[Show abstract][Hide abstract] ABSTRACT: Background:
The combination of ataxia and hypogonadism was first described more than a century ago, but its genetic basis has remained elusive.
We performed whole-exome sequencing in a patient with ataxia and hypogonadotropic hypogonadism, followed by targeted sequencing of candidate genes in similarly affected patients. Neurologic and reproductive endocrine phenotypes were characterized in detail. The effects of sequence variants and the presence of an epistatic interaction were tested in a zebrafish model.
Digenic homozygous mutations in RNF216 and OTUD4, which encode a ubiquitin E3 ligase and a deubiquitinase, respectively, were found in three affected siblings in a consanguineous family. Additional screening identified compound heterozygous truncating mutations in RNF216 in an unrelated patient and single heterozygous deleterious mutations in four other patients. Knockdown of rnf216 or otud4 in zebrafish embryos induced defects in the eye, optic tectum, and cerebellum; combinatorial suppression of both genes exacerbated these phenotypes, which were rescued by nonmutant, but not mutant, human RNF216 or OTUD4 messenger RNA. All patients had progressive ataxia and dementia. Neuronal loss was observed in cerebellar pathways and the hippocampus; surviving hippocampal neurons contained ubiquitin-immunoreactive intranuclear inclusions. Defects were detected at the hypothalamic and pituitary levels of the reproductive endocrine axis.
The syndrome of hypogonadotropic hypogonadism, ataxia, and dementia can be caused by inactivating mutations in RNF216 or by the combination of mutations in RNF216 and OTUD4. These findings link disordered ubiquitination to neurodegeneration and reproductive dysfunction and highlight the power of whole-exome sequencing in combination with functional studies to unveil genetic interactions that cause disease. (Funded by the National Institutes of Health and others.).
Full-text · Article · May 2013 · New England Journal of Medicine
[Show abstract][Hide abstract] ABSTRACT: Aarskog-Scott syndrome is a rare X-linked recessive disorder with characteristic facial, skeletal, and genital abnormalities. We report on Aarskog-Scott syndrome in male dizygotic twins with an identical de novo mutation in FGD1 that resulted from germline mosaicism in the phenotypically normal mother. This is the first report of inheritance by germline mosaicism for the FGD1 gene.
No preview · Article · Aug 2011 · American Journal of Medical Genetics Part A
[Show abstract][Hide abstract] ABSTRACT: Al-Owain M, Kaya N, Al-Zaidan H, Al-Hashmi N, Al-Bakheet A, Al-Muhaizea M, Chedrawi A, Basran RK, Milunsky A. Novel intragenic deletion in OPHN1 in a family causing XLMR with cerebellar hypoplasia and distinctive facial appearance.
X-linked mental retardation (XLMR) is notably a heterogeneous condition and often poses a diagnostic challenge. The oligophrenin 1 gene (OPHN1) is a protein with a Rho-GTPase-activating domain required in the regulation of the G-protein cycle. Mutations in the OPHN1 cause XLMR with cerebellar hypoplasia and distinctive facial appearance. We report a large Saudi family of four boys and one girl affected with XLMR. The boys had moderate MR, seizure disorder, facial dysmorphism, and cerebellar vermis hypoplasia. The girl had mild MR, seizures, and mild cerebellar hypoplasia. A novel deletion of at least exons 7–15 was identified by polymerase chain reaction analysis and multiple ligation probe amplification of the OPHN1 gene. The array comparative genomic hybridization further delineated approximately 68 kb deletion of the 7–15 exons and nearly half of intron 15. In addition, the X-inactivation confirmed random pattern in the girl. Although the affected boys have remarkably similar phenotype, there was some variability in the severity of the seizure disorder and the cerebellar hypoplasia. The report confirms the previous findings that carrier females may be symptomatic.
No preview · Article · Apr 2011 · Clinical Genetics
[Show abstract][Hide abstract] ABSTRACT: Renpenning syndrome is a well-described X-linked condition associated with multiple congenital anomalies and intellectual disability [OMIM 309500]. Typical signs include microcephaly, dysmorphic features, short stature, small testes, and lean body build. Renpenning syndrome is caused by mutations in the polyglutamine binding protein 1 (PQBP1) gene. Missense mutations, insertions, deletions, and duplications within the gene have been well-described. We present a 47-year-old male with clinical features resembling Renpenning syndrome. He has moderate intellectual disability, seizures since infancy, short stature, small testes, and dysmorphic features. Of note, our patient is normocephalic. A CT scan at 14 years of age showed cerebral atrophy. He had previously been verbally communicative and had few behavioral issues. Recently, our patient has regressed and has become uncommunicative, displaying little and unclear speech. He now exhibits memory and recognition loss and is uncooperative, aggressive, self-abusive, and incontinent. The reason for his regression within the past 4 years is unclear. SNP microarray analysis (500K) revealed a 4.7 Mb duplication at Xp11.22-p11.23. Multiple ligation probe amplification (MLPA) of the PQBP1 gene contained within this duplicated region confirmed a duplication of the entire PQBP1 gene. Multiple other genes are duplicated within this 4.7 Mb region and may contribute to his phenotype.
Preview · Article · Jan 2011 · American Journal of Medical Genetics Part A
[Show abstract][Hide abstract] ABSTRACT: We report the case of a 15-year-old girl who presented to a pediatric endocrinology clinic for delayed puberty with no signs of secondary sexual development. Her past medical history was significant for bilateral colobomas, inner-ear anomalies, hearing loss, and anosmia. Genetic testing revealed a novel de novo mutation in the CHD7 gene, one of the causative genes in CHARGE syndrome (coloboma, heart disease, choanal atresia, retarded growth and development and/or central nervous system anomalies, genital anomalies and/or hypogonadism, and ear anomalies and/or deafness). We review the distinction between hypogonadotrophic hypogonadism and hypergonadotrophic hypogonadism and discuss the availability of molecular genetic testing for idiopathic hypogonadotrophic hypogonadism. CHD7 mutations have also been found in some patients with Kallmann syndrome, hypogonadotrophic hypogonadism, and anosmia, and we discuss the overlap between this syndrome and CHARGE syndrome. With the increased availability of genetic testing for a variety of disorders, it is important for pediatricians to become familiar with interpreting genetic test results. Finally, we illustrate that Bayes' theorem is a useful statistical tool for interpreting novel missense mutations of unknown significance.
[Show abstract][Hide abstract] ABSTRACT: We report a girl with a de novo pure partial trisomy 21 with some clinical features of Down syndrome. The girl patient presented a flat broad face, brachycephaly, and a flat nasal bridge. She also had upwardly slanted palpebral fissures, epicanthal folds, blepharitis, brushfield spots, and strabismus. Her mouth was wide with downturned corners, prominent lower lip, narrow and furrowed tongue, and short palate. G-banded chromosomal analysis of metaphases in cells from both skin and blood showed a 46,XX karyotype with additional chromosomal material on the distal short arm of one chromosome 21. Parental chromosomes were normal. Molecular analyses with the short-tandem-repeat (STR) marker D21S2039 (interferon-alpha/beta receptor [IFNAR]) (21q22.1) showed a triallelic pattern. Subtelomeric fluorescent in situ hybridization (FISH) analyses, LSI 13 (retinoblastoma 1 [RB1])/LSI 21(21q22.13-q22.2), and whole chromosome painting probes specific for chromosome 21 showed trisomy for the segment 21q22.13-21q22.2 due to a de novo intrachromosomal duplication. A 500K SNP microarray analysis was then performed and revealed a 13-Mb duplication of 21q22.11-qter. This duplicated material had been translocated onto the end of the "p" arm of one of the chromosome 21s. The karyotype was provisionally defined as 46,XX,add(21)(p12).ish der (21)t(21;21)(p12;q22.11)(WCP21q+,PCP21q++,D215259/D21S341/D21S342++)dn. At the age of 4 years and 10 months, a comprehensive psychological examination was performed and the diagnostic criteria for mental retardation were not fulfilled. In comparison with previously published cases of pure partial trisomy 21, this is a rare finding. Additional studies of such rare patients should aid in the study of the pathogenesis of Down syndrome.
No preview · Article · Feb 2010 · Genetic Testing and Molecular Biomarkers
[Show abstract][Hide abstract] ABSTRACT: A balanced complex chromosome rearrangement (CCR) involving three chromosomes is rare and may lead to different types of aneuploid germ cells. We report here a 14-year follow-up of a boy with a karyotype defined as 46,XY,der(18)t(6;13;18)(q21;q21.32;q22.3).ish der(18)(13qter+,18qter-) characterized by multiple congenital abnormalities, including distinctive minor facial anomalies, short neck, abnormalities of the extremities, anogenital abnormalities, flexion contractures, especially at extremities, and severe mental and growth retardation. Chromosome analysis in the mother showed a CCR involving chromosomes 6, 13, and 18. This CCR was the result of a three-break rearrangement, and the derivative chromosome 13 consisted of parts of chromosomes 18 and 13. The karyotype of the child was not balanced, and resulted in partial trisomy for 13q and partial monosomy for 18q detected prenatally by conventional and molecular cytogenetics. Although such a karyotype and its phenotype have not previously been reported, we have compared the clinical and cytogenetic data from our patient with previously described cases of partial trisomy 13q and monosomy 18q despite different break points. We are presenting a new CCR in a woman with normal phenotype with a history of four early abortions and a long follow-up of her malformed newborn with partial 13q trisomy and 18q monosomy.
No preview · Article · Jun 2009 · Genetic Testing and Molecular Biomarkers
[Show abstract][Hide abstract] ABSTRACT: The objective of the study was to report experience with prenatal molecular diagnosis of tuberous sclerosis complex (TSC).
Sequential deoxyribonucleic acid (DNA) studies were performed on amniotic fluid cells and chorionic villi from 50 pregnant women at risk for having a child with TSC. Mutations were determined by gene sequencing and deletion/duplication analysis of the 2 TSC genes.
DNA analysis was successful in 48 of 50 tested fetuses. Mutations were precisely identified in a family member (24) (TSC1 ; TSC2 ) and/or fetus (11) (TSC1 ; TSC2 ). Novel mutations were found in 19 individual families, and a probable polymorphism was noted in 4. Second-trimester ultrasound detected 18 fetuses with cardiac rhabdomyomas. There was insufficient DNA in 1, whereas 8 of 17 (47%) had a mutation, 6 (75%) being in TSC2. In 4 of 18 cases, a mutation was detected in the fetus for the first time despite a parent known to have TSC.
The value and utility of prenatal diagnosis of TSC by DNA analysis was demonstrated by the results in this series of 50 pregnancies in women at risk of having affected offspring. A family history of TSC or detection of fetal cardiac rhabdomyoma should prompt genetic evaluation and counseling of parents and the option of prenatal diagnosis.
No preview · Article · Apr 2009 · American journal of obstetrics and gynecology
[Show abstract][Hide abstract] ABSTRACT: We present clinical and developmental data on a patient with a de novo recombinant pseudodicentric bisatellited chromosome 22 associated with a partial trisomy 22pter-22q12.1. The patient was evaluated at birth and followed-up until 21 years of age. Clinical findings include facial and digital dysmorphism, hydrocephalus and postnatal-onset growth deficiency. The patient showed bilateral microphthalmia with severe palpebral ptosis and coloboma of the iris and left optic nerve. She also has skeletal and neurological abnormalities, cholesteatoma and seizures. She had absence of speech, poor mobility, poor vision and required help with all daily living skills. Conventional chromosome GTG banded analysis showed that the proband had an abnormal karyotype:46,XX,add(22)(q13). Fluorescence in situ hybridization (FISH) analyses and microsatellite markers for DNA polymorphism study ascertained the karyotype as 46,XX,add(22)(q13.3).ish psu dic(22;22)(q13.3;q12.1)(D14Z1/D22Z1++, N25++, ARSA+, PCP22q+). The recombinant chromosome was stable and present in all cells examined. The paternal origin of the psu dic(22;22) chromosome was determined by using five highly polymorphic microsatellite markers located to the region of chromosome 22q11.2-22q13.33. A 22q13.3 monosomy was ruled out with 22q13.3 cosmid probes covering the terminal 22q-140Kb. The proband carried a recombinant pseudodicentric bisatellited chromosome psu dic(22;22)(q13.3;q12.1). To our knowledge, this is the first report of such rearrangement resulting in partial trisomy 22pter-22q12.1.
No preview · Article · Feb 2008 · European Journal of Medical Genetics
[Show abstract][Hide abstract] ABSTRACT: Supernumerary marker chromosomes (SMCs) without detectable alphoid DNA are predicted to have a neocentromere and have been referred to as mitotically stable neocentromere marker chromosomes (NMCs). Here we report the molecular cytogenetic characterization of a new case of Pallister-Killian syndrome (PKS) in a boy with an analphoid, inverted duplicated NMC derived from 12pter-->12p11.22 in his fibroblasts by using high-resolution comparative genetic hybridization (HR-CGH), multiplex fluorescent in situ hybridization (FISH) and bacterial artificial chromosome (BAC)-FISH mapping analyses with various alpha-satellite DNA probes, subtelomere probes and BAC-DNA probes. Precise identification of SMCs and NMCs is of essential importance in genetic counseling. HR-CGH is a more informative and often a faster way of precisely identifying the origin of SMCs. This case is the third report of PKS with an NMC containing an inverted duplication of partial 12p with available clinical data. These observations may help to determine the critical region for PKS and the mechanisms leading to the origin of the NMC derived from 12pter-->12p11.22 - a region that appears to be susceptible to the formation of neocentromeres. The use of subtelomeric probe PCP12p in buccal cells appears superior to the use of the centromere probe D12Z3 for the diagnosis of the PKS.
No preview · Article · Nov 2007 · Clinical Genetics
[Show abstract][Hide abstract] ABSTRACT: Partial trisomy 12q and monosomy 12p lead to multiple malformation syndromes. Only four cases were previously reported with the association of these two aneusomies resulting from a familial pericentric inversion of chromosome 12. We report on the clinical, cytogenetic and molecular findings in a boy with an unbalanced karyotype which resulted from a familial pericentric inversion of chromosome 12. The patient was evaluated at birth and followed up until 14 years of age. He showed severe mental retardation, seizures, and dysmorphic features related both to a trisomy 12q and a monosomy 12p. Chromosome breakpoint BAC-FISH mapping revealed that the rec(12) chromosome had a terminal deletion of a 6.7Mb region extending from 12pter to 12p13.31 and a duplicated region of 19.8Mb extending from 12qter to 12q24.13. The findings from the case reported here emphasize the occurrence of some consistent clinical features and illustrate the deficiencies associated with the recombinants from the inversion inv(12)(p13.31q24.13)mat.
No preview · Article · May 2007 · European Journal of Medical Genetics
[Show abstract][Hide abstract] ABSTRACT: To describe a de novo complex chromosome rearrangement(CCR) detected prenatally and studied afterbirth.
Conventional cytogenetics and fluorescent in situ hybridization (FISH) were performed on amniotic fluid and peripheral blood. High-resolution comparative genomic hybridization (HR-CGH) analysis was made postnatally.
Prenatal/postnatal cytogenetic, FISH and HR-CGH analyses revealed an apparently balanced de novo CCR ascertained as 46,XY,t(2; 3;9)(q21;p24;q22),der(5)inv(5)(?p11q13)t(5; 11)(?p13;q25),ins(5; 3)(?p13;?p23p24). At 9 months,the child has neither congenital anomalies nor evidence of delayed psychomotor development.
Our report describes a rare CCR detected prenatally and shows the usefulness of FISH and CGH in complementing conventional cytogenetics.
No preview · Article · Feb 2007 · Fetal Diagnosis and Therapy
[Show abstract][Hide abstract] ABSTRACT: Waardenburg syndrome (WS) is an autosomal-dominant neurocristopathy characterized by sensorineural hearing loss, pigmentary abnormalities of the iris, hair, and skin, and is responsible for about 3% of congenital hearing loss. Point mutations in PAX3 have been identified in more than 90% of affected individuals with WS Type 1/WS Type 3. MITF point mutations have been identified in 10-15% of individuals affected with WS Type 2 (lacking dystopia canthorum). Multiplex ligation-dependent probe amplification (MLPA) is now a standard technology in the molecular genetics laboratory to detect copy number changes in targeted genes. We employed MLPA for PAX3 and MITF in a cohort of patients submitted with a diagnosis of WS1, 2 or 3 who were sequence negative for PAX3 and/or MITF. All coding exons of PAX3 and exons 1, 2, 3, and 10 of MITF were included in the MLPA assay. MLPA on 48 patients with WS 1 or 3 revealed 3 PAX3 whole gene deletions (2 WS1; 1 WS3), 2 PAX3 partial gene deletions [WS1, exon 1 and promoter (1st report); WS1, exons 5-9], and 1 partial MITF deletion ("WS1", exons 3-10) (6/48 approximately 12.5%). MLPA on 41 patients with WS2 and 20 patients submitted with a diagnosis of either WS1 or WS2 revealed no copy number changes. The detection of both partial and whole gene deletions of PAX3/MITF in this clinical cohort increases the mutation detection yield by at least 6% and supports integrating MLPA into clinical molecular testing primarily for patients with WS1 and 3.
[Show abstract][Hide abstract] ABSTRACT: The study's purpose was to understand the molecular basis for different clinical phenotypes of the 5T variant, a tract of 5 thymidines in intron 8 of the cystic fibrosis transmembrane conductance regulator (CFTR) gene, which disrupts processing of CFTR mRNA and reduces synthesis from the corresponding CFTR alleles.
We analyzed the polymorphic TG dinucleotide repeat adjacent to the 5T variant in intron 8 and the codon 470 in exon 10. Patients selected for this study were positive for both the 5T variant and the major cystic fibrosis mutation, Delta F508. Almost all Delta F508 mutation alleles occur in a 10TG-9T-470M haplotype. Therefore, it is possible to determine the haplotype of the 5T variant in trans.
Of the 74 samples analyzed, 41 (55%) were 11TG-5T-470M, 31 (42%) were 12TG-5T-470V, and 2 (3%) were 13TG-5T-470M. Of the 49 cases for which we had clinical information, 17.6% of females (6/34) and 66.7% of males (10/15) showed symptoms resembling atypical cystic fibrosis. The haplotype with the highest penetrance in females (42% or 5/12) and more than 80% (5/6) in males is 12TG-5T-470V. We also evaluated 12 males affected with congenital bilateral absence of vas deferens and positive for the 5T variant; 10 of 12 had the 12TG-5T-470V haplotype.
Overall, the 5T variant has a milder clinical consequence than previously estimated in females. The clinical presentations of the 5T variant are associated with the 5T-12TG-470M haplotype.
Full-text · Article · Jul 2006 · Genetics in Medicine
[Show abstract][Hide abstract] ABSTRACT: Most cystic fibrosis mutation screening methods do not detect large exon deletions or duplications in the cystic fibrosis transmembrane regulator gene. We looked for such mutations in congenital bilateral absence of the vas deferens patients in whom routine screening assays had identified only one or no cystic fibrosis transmembrane regulator gene mutations.
DNA samples from 48 men with congenital bilateral absence of the vas deferens were tested for exonic deletions and duplications in the cystic fibrosis transmembrane regulator gene using a laboratory-developed semiquantitative fluorescent PCR assay.
Semi-quantitative fluorescent PCR identified a large deletion in one (2%) of the 48 patients. This patient, previously characterized as carrying only the IVS8-5T mutation, was found to have a deletion of exons 22-24 of the cystic fibrosis transmembrane regulator gene. In a second patient with the IVS8-5T mutation, we identified a one-base pair insertion in exon 17b that disrupted the reading frame.
Analysis of the cystic fibrosis transmembrane regulator gene for exon deletions and duplications should be included for complete study of CBAVD patients, especially those considering assisted reproduction.
Preview · Article · Mar 2006 · Genetics in Medicine
[Show abstract][Hide abstract] ABSTRACT: Rapid fluorescence in situ hybridization (FISH) performed on 1,788 amniocenteses, using Aneuvision (Vysis) probes for chromosomes 13, 18, 21, X, and Y, over several years, yielded 115 cases with percentages of aneuploidy between 4 and 100%. All cases above 60% were confirmed to be positive by chromosome analysis. Fifteen of forty-one cases that would be considered inconclusive by generally accepted criteria (i.e. with less than 60% of cells with an abnormal signal pattern) revealed lower cutoffs to be positive when confirmed by chromosome analysis. For trisomy 21, 6 cases with percentages from 36 to 57% were positive; 4 of 7 cases with percentages from 22.5 to 33% were positive; 11 cases with percentages of 13% or less were negative. Similar trends were found for aneuploidies of 13, 18, X, and Y. However, the number of abnormal cases is still too small to determine definitive cutoffs in the <60% gray zone. An average of 57 metaphases was analyzed for cases with FISH percentages below 60%. Despite the wide range of abnormal FISH percentages for chromosomally positive cases, we found no examples of autosomal mosaicism in this series. Although sex chromosome mosaicism was cytogenetically evident in several cases, there was little direct correlation between cytogenetic and rapid FISH results. FISH results involving sex chromosomes were more frequently confounded by maternal cell contamination and other technical factors.
No preview · Article · Feb 2006 · Fetal Diagnosis and Therapy